NAC candidate gene marker for bgm-1 and interaction with QTL for resistance to Bean golden yellow mosaic virus in common bean

Authors: SOLER-GARZON, A - Washington State University; OLADZADABBASABADI, A - North Dakota State University; BEAVER, J - University Of Puerto Rico; BEEBE, S - International Center For Tropical Agriculture (CIAT); LEE, R - North Dakota State University; LOBATON, J - International Center For Tropical Agriculture (CIAT); MACEA, E - International Center For Tropical Agriculture (CIAT); MCCLEAN, P - North Dakota State University; RAATZ, B - International Center For Tropical Agriculture (CIAT); ROSAS, J - Zamorano, Panamerican School Of Agriculture; Song, Qijian; Miklas, Phillip - Phil

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/3/2021
Publication Date: 3/25/2021
Citation: Soler-Garzon, A., Oladzadabbasabadi, A., Beaver, J., Beebe, S., Lee, R., Lobaton, J., Macea, E., Mcclean, P., Raatz, B., Rosas, J.C., Song, Q., Miklas, P.N. 2021. NAC candidate gene marker for bgm-1 and interaction with QTL for resistance to Bean golden yellow mosaic virus in common bean. Frontiers in Plant Science. 12. Article 628443. https://doi.org/10.3389/fpls.2021.628443.
DOI: https://doi.org/10.3389/fpls.2021.628443

Interpretive Summary: Bean golden yellow mosaic virus (BGYMV) plagues common bean production in Central America and the Caribbean. BGYMV epidemics are influenced by prevalence of the whitefly vector in the field. Severe BGYMV epidemics can result in up to 100% crop loss. Utilizing common bean varieties pyramiding different host resistances is a critical strategy to control the virus. Previous studies discovered several genomic regions including bgm-1, BGY4.1 and BGY7.1 that conditioned high levels of resistance against leaf yellowing, mosaic, chlorosis or pod deformation, however, the genes in these regions were unmapped or mapped with loosely-linked markers, making it impossible to efficiently tag and transfer these genes to other cultivars through marker-assisted selection. In this study, we found a 5-bp deletion in a candidate gene hvul.003G027100 on chromosome Pv03 corresponded with the resistance at one of most important genomic region (bgm-1) and developed markers to track the resistance for this genes and the genes at BGY4.1 and BGY7.1 regions. The information will not only lead to the better understanding of the mechanism controlling the resistance, but also facilitate molecular breeding selection for BGYMV resistance at private and public breeding programs and accelerate common bean breeding.

Technical Abstract: Genetic resistance is the primary means for control of Bean golden yellow mosaic virus (BGYMV) in common bean (Phaseolus vulgaris L.). Breeding for resistance is difficult because of sporadic and uneven infection across field nurseries. We sought to facilitate breeding for BGYMV resistance by improving MAS for the recessive bgm-1 gene and to identify and develop MAS for quantitative trait loci (QTL) conditioning resistance. Genetic linkage mapping in two recombinant inbred line populations, and GWAS in a large breeding population and two diversity panels revealed a candidate gene for bgm-1 and three QTL BGY4.1, BGY7.1 and BGY8.1 on independent chromosomes. A mutation (5 bp deletion) in a NAC (No Apical Meristem) domain transcriptional regulator superfamily protein gene hvul.003G027100 on chromosome Pv03 corresponded with the recessive bgm-1 resistance allele. The 5 bp deletion (occurred post-domestication) starting at 19 bp in the second exon is expected to cause a stop codon at 69 bp disrupting further translation of the gene. A Tm-shift assay marker named PvNAC1 was developed to track bgm-1. PvNAC1 corresponded with bgm-1 across ~1000 lines which traces bgm-1 back to a single landrace ‘Garrapato’ from Mexico. BGY8.1 has no effect on its own but exhibited a major effect when combined with bgm-1. BGY4.1 and BGY7.1 acted additively, and they enhanced the level of resistance when combined with bgm-1. Tm-shift assay markers were generated for MAS of the QTL but their effectiveness requires further validation.